LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  1 by 1 by 1 MPI processor grid
  32 atoms
  Time spent = 0.000318766 secs

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

change_box  all boundary p f p

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 0.1
variable c_t        equal 0.1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0

fix          2 all enforce2d
fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.15685
  ghost atom cutoff = 6.15685
  binsize = 3.07843, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes
Step KinEng PotEng TotEng Press 
       0     0.484375         0.25     0.734375 0.0067274306 
    1000   0.51467204 0.00099202506   0.51566407  0.013452386 
    2000   0.55674899 0.0040762275   0.56082522 0.0034529066 
    3000    0.7546177   0.02259362   0.77721132  0.003650781 
    4000   0.72710218   0.10284108   0.82994326 0.0059629371 
    5000    0.5771012  0.069052145   0.64615335 0.00053937622 
    6000   0.53848154  0.041891239   0.58037277 0.0018693312 
    7000   0.61777556  0.033379829   0.65115538 0.0027584418 
    8000   0.47427227  0.059558934    0.5338312  0.017087187 
    9000   0.46822364  0.064382578   0.53260622  0.023258465 
   10000   0.46511051  0.027799371   0.49290988  0.015319493 
   11000   0.58686703  0.088016891   0.67488392 0.0088428936 
   12000   0.49962603   0.09879099   0.59841702 0.00074311497 
   13000   0.53160049  0.069625775   0.60122626  0.017019775 
   14000   0.49574902  0.041214164   0.53696318 0.0060355978 
   15000   0.56620415   0.13621516   0.70241931  0.045583297 
   16000   0.40942564   0.11469877   0.52412441  0.029905784 
   17000     0.608066  0.096938921   0.70500493  0.018509814 
   18000   0.45622168  0.057018077   0.51323975 0.0034035281 
   19000   0.48763322  0.057832224   0.54546545 0.0022972169 
   20000   0.41577025   0.14480819   0.56057844  0.023882542 
   21000   0.58565738    0.1601676   0.74582498   0.01702799 
   22000   0.60430354   0.16740706    0.7717106 -0.0047632836 
   23000   0.45659601   0.13740896   0.59400497    0.0191143 
   24000   0.42741367   0.25490516   0.68231884  0.051459175 
   25000   0.40851048  0.077823072   0.48633355  0.024392284 
   26000   0.53392894   0.14504323   0.67897217  0.028964572 
   27000   0.39775205   0.13101153   0.52876358 0.0080564916 
   28000   0.63138106   0.17706612   0.80844718  0.017594524 
   29000   0.57897788   0.26855503   0.84753292  0.019310624 
   30000   0.37401002    0.2274666   0.60147663 0.0044804008 
   31000   0.60924323   0.23142663   0.84066986  0.088271242 
   32000   0.60310397   0.35719837   0.96030234 0.0096762289 
   33000   0.47468105   0.17727177   0.65195282 0.0078486602 
   34000   0.42270829   0.20131235   0.62402064  0.090216203 
   35000   0.49578606    0.1697981   0.66558416  0.079099134 
   36000   0.50744538   0.29600416   0.80344954  0.018819487 
   37000   0.66728184   0.28166655   0.94894838  -0.01679437 
   38000   0.38972905   0.25798163   0.64771068  0.040442456 
   39000   0.38292839   0.21774389   0.60067228  0.016754932 
   40000   0.61770336   0.34202184    0.9597252   0.10986262 
   41000   0.42252651   0.13424708    0.5567736  0.040987711 
   42000   0.67513868   0.29515562    0.9702943 0.0013757417 
   43000   0.36768915   0.20349753   0.57118668  0.031443504 
   44000   0.49371025  0.095615653    0.5893259  0.032289477 
   45000   0.42144079   0.28894639   0.71038718  0.040302569 
   46000   0.36360136   0.33117431   0.69477567  0.010881881 
   47000    0.4206309   0.19557595   0.61620685  0.051137535 
   48000    0.4131465   0.37027912   0.78342561   0.11903042 
   49000     0.544703   0.38013565   0.92483865  0.054939742 
   50000   0.47394272   0.32384493   0.79778764  0.088363602 
   51000   0.55377533   0.38103395   0.93480927  0.097981664 
   52000   0.60648433   0.30877364   0.91525797  0.088877781 
   53000   0.62933509   0.33187159   0.96120668   0.10275954 
   54000   0.55077522   0.39050008   0.94127529  0.066721412 
   55000   0.41646397   0.34545572   0.76191969  0.011056796 
   56000   0.44244954   0.39274744   0.83519698  0.039963853 
   57000   0.41963092   0.33483982   0.75447073  0.032555938 
   58000   0.37941475   0.36905323   0.74846798  0.043952263 
   59000   0.53008564   0.32843795   0.85852359  0.080787301 
   60000   0.43408908   0.19840268   0.63249176   0.06421165 
   61000   0.56287814   0.31500577   0.87788391   0.12031895 
   62000    0.5185192   0.18275672   0.70127592 -0.0086212356 
   63000   0.57275413   0.45147395    1.0242281  0.054617465 
   64000   0.28322907   0.33687722   0.62010629   0.07268947 
   65000   0.40230876   0.37989067   0.78219943 -0.029604066 
   66000   0.58601209   0.52721274    1.1132248 -0.00037054404 
   67000   0.52669356   0.44276199   0.96945554   0.18969356 
   68000   0.41566831   0.47320489    0.8888732  0.040635264 
   69000   0.52140574    0.4261935   0.94759923  0.016566201 
   70000   0.42034133   0.55867009   0.97901142  0.047465899 
   71000   0.48720036   0.43749264     0.924693   0.15984789 
   72000    0.5244238   0.55854139    1.0829652   0.10155994 
   73000   0.69990219   0.57313852    1.2730407   0.11108648 
   74000   0.38274347   0.23359664   0.61634011  0.027968087 
   75000   0.47493369   0.49472607   0.96965976   0.10961568 
   76000   0.57064727   0.37996383    0.9506111  0.034746271 
   77000   0.50401727   0.34437588   0.84839315  0.015116686 
   78000   0.59504118   0.44154772    1.0365889  0.059341875 
   79000    0.4920801   0.58935767    1.0814378   0.12139906 
   80000   0.56992818   0.38916606   0.95909424  0.073618074 
   81000   0.38446945   0.77314417    1.1576136   0.12173381 
   82000   0.48734531   0.56198203    1.0493273    0.1080115 
   83000    0.5516933   0.56743096    1.1191243   0.13936805 
   84000   0.53336893   0.62914863    1.1625176 0.0084970895 
   85000   0.46456977   0.77446084    1.2390306   0.18024688 
   86000   0.58067599   0.53109608    1.1117721  0.012492021 
   87000   0.55096446   0.61715622    1.1681207   0.13264723 
   88000   0.56548774   0.74463701    1.3101247   0.14491188 
   89000   0.52492634   0.58482194    1.1097483   0.21155245 
   90000   0.64973565   0.85514474    1.5048804  0.036911953 
   91000   0.55367722   0.74046971    1.2941469   0.23918851 
   92000   0.44863249   0.56773761    1.0163701 0.00042860088 
   93000   0.64728356   0.66594086    1.3132244 0.0022850006 
   94000   0.65255497   0.82136644    1.4739214   0.10037643 
   95000   0.62266654   0.82642147     1.449088   0.11964602 
   96000   0.50656004   0.83312844    1.3396885  0.078491084 
   97000   0.47126712   0.70469684     1.175964   0.12956056 
   98000   0.48661103    1.0121726    1.4987837  0.043537851 
   99000   0.48379797    0.9520931    1.4358911  0.082047522 
  100000   0.54266361    1.0959698    1.6386334  -0.13092175 
Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms

Performance: 2242290.202 tau/day, 25952.433 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.3917     | 2.3917     | 2.3917     |   0.0 | 62.07
Neigh   | 0.012386   | 0.012386   | 0.012386   |   0.0 |  0.32
Comm    | 0.11307    | 0.11307    | 0.11307    |   0.0 |  2.93
Output  | 0.0010369  | 0.0010369  | 0.0010369  |   0.0 |  0.03
Modify  | 1.246      | 1.246      | 1.246      |   0.0 | 32.34
Other   |            | 0.08895    |            |       |  2.31

Nlocal:    32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    55 ave 55 max 55 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 55
Ave neighs/atom = 1.71875
Neighbor list builds = 2886
Dangerous builds = 0
Total wall time: 0:00:03
